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Detailed information for vg0720714007:

Variant ID: vg0720714007 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 20714007
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTTGGTTGCCTGCTTAGGCCTCCCAGCCTGTCCACGCGGATGCAAAAAAAGCCCCTCAGCCAGGCCCGACAGAAACGGCCGATTCCCACTTCGCTGCTC[A/G]
GCCTGGCTCGACTGATGCACACCGCTGCACCCGCGCCTGCACCCGCGCGTGCAACTCACGGAGGATGGGGTCACCGTTGCTTCCCAGAATCGCTCCCTCC

Reverse complement sequence

GGAGGGAGCGATTCTGGGAAGCAACGGTGACCCCATCCTCCGTGAGTTGCACGCGCGGGTGCAGGCGCGGGTGCAGCGGTGTGCATCAGTCGAGCCAGGC[T/C]
GAGCAGCGAAGTGGGAATCGGCCGTTTCTGTCGGGCCTGGCTGAGGGGCTTTTTTTGCATCCGCGTGGACAGGCTGGGAGGCCTAAGCAGGCAACCAAAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.80% 10.90% 2.64% 3.60% NA
All Indica  2759 97.10% 2.20% 0.72% 0.00% NA
All Japonica  1512 54.40% 28.20% 6.08% 11.24% NA
Aus  269 98.50% 0.70% 0.74% 0.00% NA
Indica I  595 97.80% 1.80% 0.34% 0.00% NA
Indica II  465 97.00% 2.60% 0.43% 0.00% NA
Indica III  913 97.20% 2.10% 0.77% 0.00% NA
Indica Intermediate  786 96.40% 2.40% 1.15% 0.00% NA
Temperate Japonica  767 24.60% 49.00% 6.26% 20.08% NA
Tropical Japonica  504 93.10% 2.80% 3.97% 0.20% NA
Japonica Intermediate  241 68.50% 15.40% 9.96% 6.22% NA
VI/Aromatic  96 79.20% 10.40% 10.42% 0.00% NA
Intermediate  90 80.00% 18.90% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0720714007 A -> DEL N N silent_mutation Average:87.284; most accessible tissue: Minghui63 flag leaf, score: 96.905 N N N N
vg0720714007 A -> G LOC_Os07g34550.1 intron_variant ; MODIFIER silent_mutation Average:87.284; most accessible tissue: Minghui63 flag leaf, score: 96.905 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0720714007 A G -0.14 -0.11 -0.09 -0.1 -0.12 -0.12

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0720714007 NA 6.08E-07 mr1013 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 NA 5.54E-07 mr1031 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 NA 3.57E-06 mr1045 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 NA 4.10E-06 mr1056 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 1.50E-08 NA mr1071 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 5.19E-07 NA mr1140 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 NA 7.25E-08 mr1163 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 1.91E-07 NA mr1203 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 3.14E-06 NA mr1395 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 8.06E-06 8.04E-06 mr1494 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 NA 4.42E-06 mr1555 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 3.56E-06 NA mr1618 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0720714007 NA 6.81E-06 mr1596_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251